In addition to the stipulations listed below, I have also noticed
that apbs can't handle a pdb file that has coordinate columns that
touch each other such as this example:
N GLY A 38 66.914
66.219-103.497 1.00 18.01
ATOM 79 CA GLY A
38 66.309 66.763-104.698
1.00 20.04 A
ATOM 80 C GLY A
38 65.598 68.007-104.199
1.00 20.96 A
O GLY A 38 64.432
68.267-104.508 1.00 23.61
I've needed to transform the coordinates of my molecule so that
this kind of thing doesn't happen.
(realspace_transform.inp in CNS works.)
Hope this helps.
You have to see if you are getting the .dx file. The default of
the program is to put it at the same directory where it was installed,
along with the other temporary files: .in, .pqr and .pdb. In case of
not, I got the same problem and the solution was: the PDB that you
load can`t have chain ID, the aminoacids can`t have alternate
conformations and the program only accepts the standard residues. If
everything is all right with your PBD, after run the APBS you gotta
have the .dx at this directory. Once you got the .dx (the pymol will
show the apbs.map) click at the update (on Visualization) and then
Hope this help!
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